Variant report

Variant	rs9975404
Chromosome Location	chr21:47159212-47159213
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:47158414..47160946-chr21:47163117..47165141,2	MCF-7	breast:
2	chr21:47061487..47064161-chr21:47158776..47160819,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000183570	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs1029014	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12151963	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12483701	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1467758	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17004799	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1964928	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1989537	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2150460	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2183595	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2183596	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2183601	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2838973	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2838974	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2838976	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2838978	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2838981	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2838982	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2838983	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2838985	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2838988	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2838989	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2838990	0.81[ASN][1000 genomes]
rs2838991	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2838992	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2838993	0.81[ASN][1000 genomes]
rs28583990	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28625750	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3367	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3920695	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4347938	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4434082	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4818795	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4818797	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4819144	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55912508	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55923134	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55957843	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56012600	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56213918	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56288252	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56300316	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56323347	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57057834	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57282159	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57328058	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57501220	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57990579	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58368336	0.85[EUR][1000 genomes]
rs58925015	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60604183	0.81[ASN][1000 genomes]
rs60988006	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61329313	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62213277	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62215031	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62215035	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62215040	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62215047	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62215048	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67565220	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs725358	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7279909	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7280560	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7283803	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7410008	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs744506	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs767137	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8133966	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs914241	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9306139	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9637169	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9647229	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9647230	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9974491	0.81[ASN][1000 genomes]
rs9976200	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9976878	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9977908	0.83[ASN][1000 genomes]
rs9978078	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9978158	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9978740	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9978882	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9981586	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531546	chr21:46504151-47411772	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
2	nsv1058665	chr21:46719445-47634282	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	91 gene(s)	inside rSNPs	diseases
3	nsv544486	chr21:46719445-47634282	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	91 gene(s)	inside rSNPs	diseases
4	nsv1059230	chr21:46956877-47907990	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
5	nsv544491	chr21:46956877-47907990	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
6	nsv1058472	chr21:47027823-47797326	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
7	nsv544492	chr21:47027823-47797326	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
8	nsv1063957	chr21:47090475-47168291	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
9	nsv1062702	chr21:47095762-47169369	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
10	nsv544493	chr21:47095762-47169369	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
11	esv3328690	chr21:47159050-47159598	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
12	esv3441449	chr21:47159125-47159412	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9975404	PCBP3	cis	lung	GTEx
rs9975404	PCBP3	cis	Muscle Skeletal	GTEx
rs9975404	PCBP3	cis	Nerve Tibial	GTEx
rs9975404	PCBP3	cis	Heart Left Ventricle	GTEx

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47135600-47165000	Weak transcription	Primary T cells from cord blood	blood
2	chr21:47144200-47167600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr21:47146600-47159600	Weak transcription	Spleen	Spleen
4	chr21:47146600-47160000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr21:47151800-47164800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr21:47152600-47160400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr21:47153200-47165400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr21:47154400-47160000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr21:47156600-47168000	Weak transcription	Brain Angular Gyrus	brain
10	chr21:47156800-47164800	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr21:47157000-47168200	Weak transcription	Brain Hippocampus Middle	brain
12	chr21:47157600-47165000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr21:47157800-47159600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr21:47157800-47160000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr21:47157800-47160800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr21:47157800-47167400	Weak transcription	HSMMtube	muscle
17	chr21:47158000-47159600	Weak transcription	Thymus	Thymus
18	chr21:47158000-47165400	Weak transcription	Dnd41	blood
19	chr21:47158400-47159800	Enhancers	Primary T cells fromperipheralblood	blood
20	chr21:47158600-47159800	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr21:47158600-47160200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr21:47158800-47169800	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr21:47159000-47159400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr21:47159000-47168000	Weak transcription	Brain Anterior Caudate	brain
25	chr21:47159200-47160200	Enhancers	Fetal Thymus	thymus

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